Investigation on Cacao swollen shoot virus (CSSV) pollen transmission through cross-pollination

DNA- and RNA-based polymerase chain reaction (PCR) systems were used with Cacao swollen shoot virus (CSSV) primers designed from conserved regions of the six published genomic sequences of CSSV to investigate whether the virus is transmissible from infected trees through cross-pollination to seeds and seedlings. Pollen was harvested from CSSV infected cocoa trees and used to cross-pollinate flowers of healthy cocoa trees (recipient parents) to generate enough cocoa seeds for the PCR screening. Adequate precautions were taken to avoid cross-contamination during duplicated DNA extractions and only PCR results accompanied by effective positive and negative controls were scored. Results from the PCR analyses showed that samples of cocoa pod husk, mesocarp and seed tissues (testa, cotyledon and embryo) from the cross-pollinations were PCR negative for CSSV DNA. Sequential DNA samples from new leaves of seedlings resulting from the cross-pollinated trees were consistently PCR negative for presence of portions of CSSV DNA for over 36 months after germination. A reverse transcription-PCR analysis performed on the seedlings showed negative results, indicating absence of functional CSSV RNA transcripts in the seedlings. None of the seedlings exhibited symptoms characteristic of the CSSV disease, and all infectivity tests on the seedlings were also negative. Following these results, the study concluded that although CSSV DNA was detected in pollen from CSSV infected trees, there was no evidence of pollen transmission of the virus through cross-pollination from infected cocoa parents to healthy cocoa trees.

Facile production of ordered 3D platinum nanowire networks with “single diamond” bicontinuous cubic morphology

Direct electrochemical templating is carried out using a thin layer of a self-assembled diamond phase (QIID) of phytantriol to create a platinum film with a novel nanostructure. Small-angle X-ray scattering shows that the nanostructured platinum films are asymmetrically templated and exhibit “single diamond” morphology with Fd3m symmetry.

Neuromantic : from semi-manual to semi-automatic reconstruction of neuron morphology

The ability to create accurate geometric models of neuronal morphology is important for understanding the role of shape in information processing. Despite a significant amount of research on automating neuron reconstructions from image stacks obtained via microscopy, in practice most data are still collected manually. This paper describes Neuromantic, an open source system for three dimensional digital tracing of neurites. Neuromantic reconstructions are comparable in quality to those of existing commercial and freeware systems while balancing speed and accuracy of manual reconstruction. The combination of semi-automatic tracing, intuitive editing, and ability of visualizing large image stacks on standard computing platforms provides a versatile tool that can help address the reconstructions availability bottleneck. Practical considerations for reducing the computational time and space requirements of the extended algorithm are also discussed.

Arboreal thorn-dwelling ants use domatia morphology to partition nest sites on the savanna ant-plant, Vachellia erioloba

Nest site selection in arboreal, domatia-dwelling ants, particularly those coexisting on a single host plant, is little understood. To examine this phenomenon we studied the African savannah tree Vachellia erioloba, which hosts ants in swollen-thorn domatia. We found four ant species from different genera (Cataulacus intrudens, Tapinoma subtile, Tetraponera ambigua and an unidentified Crematogaster species). In contrast to other African ant plants, many V. erioloba trees (41 % in our survey) were simultaneously co-occupied by more than one ant species. Our study provides quantitative field data describing: (1) aspects of tree and domatia morphology relevant to supporting a community of mutualist ants, (2) how ant species occupancy varies with domatia morphology and (3) how ant colony size varies with domatia size and species. We found that Crematogaster sp. occupy the largest thorns, followed by C. intrudens, with T. subtile in the smallest thorns. Thorn age, as well as nest entrance hole size correlated closely with ant species occupant. These differing occupancy patterns may help to explain the unusual coexistence of three ant species on individual myrmecophytic trees. In all three common ant species, colony size, as measured by total number of ants, increased with domatia size. Additionally, domatia volume and species identity interact to predict ant numbers, suggesting differing responses between species to increased availability of nesting space. The proportion of total ants in nests that were immatures varied with thorn volume and species, highlighting the importance of domatia morphology in influencing colony structure.

An improved methodology for the recovery of Zea mays and other large crop pollen, with implications for environmental archaeology in the Neotropics

We present a simple sieving methodology to aid the recovery of large cultigen pollen grains, such as maize (Zea mays L.), manioc (Manihot esculenta Crantz), and sweet potato (Ipomoea batatas L.), among others, for the detection of food production using fossil pollen analysis of lake sediments in the tropical Americas. The new methodology was tested on three large study lakes located next to known and/or excavated pre-Columbian archaeological sites in South and Central America. Five paired samples, one treated by sieving, the other prepared using standard methodology, were compared for each of the three sites. Using the new methodology, chemically digested sediment samples were passed through a 53 µm sieve, and the residue was retained, mounted in silicone oil, and counted for large cultigen pollen grains. The filtrate was mounted and analysed for pollen according to standard palynological procedures. Zea mays (L.) was recovered from the sediments of all three study lakes using the sieving technique, where no cultigen pollen had been previously recorded using the standard methodology. Confidence intervals demonstrate there is no significant difference in pollen assemblages between the sieved versus unsieved samples. Equal numbers of exotic Lycopodium spores added to both the filtrate and residue of the sieved samples allow for direct comparison of cultigen pollen abundance with the standard terrestrial pollen count. Our technique enables the isolation and rapid scanning for maize and other cultigen pollen in lake sediments, which, in conjunction with charcoal and pollen records, is key to determining land-use patterns and the environmental impact of pre-Columbian societies.

Characterisation of Bolivian savanna ecosystems by their modern pollen rain and implications for fossil pollen records

The majority of vegetation reconstructions from the Neotropics are derived from fossil pollen records extracted from lake sediments. However, the interpretation of these records is restricted by limited knowledge of the contemporary relationships between the vegetation and pollen rain of Neotropical ecosystems, especially for more open vegetation such as savannas. This research aims to improve the interpretation of these records by investigating the vegetation and modern pollen rain of different savanna ecosystems in Bolivia using vegetation inventories, artificial pollen traps and surface lake sediments. Two types of savanna were studied, upland savannas (cerrado), occurring on well drained soils, and seasonally-inundated savannas occurring on seasonally water-logged soils. Quantitative vegetation data are used to identify taxa that are floristically important in the different savanna types and to allow modern pollen/vegetation ratios to be calculated. Artificial pollen traps from the upland savanna site are dominated by Moraceae (35%), Poaceae (30%), Alchornea (6%) and Cecropia (4%). The two seasonally-inundated savanna sites are dominated by Moraceae (37%), Poaceae (20%), Alchornea (8%) and Cecropia (7%), and Moraceae (25%), Cyperaceae (22%), Poaceae (19%) and Cecropia (9%), respectively. The modern pollen rain of seasonally-inundated savannas from surface lake sediments is dominated by Cyperaceae (35%), Poaceae (33%), Moraceae (9%) and Asteraceae (5%). Upland and seasonally-flooded savannas were found to be only subtly distinct from each other palynologically. All sites have a high proportion of Moraceae pollen due to effective wind dispersal of this pollen type from areas of evergreen forest close to the study sites. Modern pollen/vegetation ratios show that many key woody plant taxa are absent/under-represented in the modern pollen rain (e.g., Caryocar and Tabebuia). The lower-than-expected percentages of Poaceae pollen, and the scarcity of savanna indicators, in the modern pollen rain of these ecosystems mean that savannas could potentially be overlooked in fossil pollen records without consideration of the full pollen spectrum available.

Pollen-based differentiation of Amazonian rainforest communities and implications for lowland palaeoecology in tropical South America

An ongoing controversy in Amazonian palaeoecology is the manner in which Amazonian rainforest communities have responded to environmental change over the last glacial–interglacial cycle. Much of this controversy results from an inability to identify the floristic heterogeneity exhibited by rainforest communities within fossil pollen records. We apply multivariate (Principal Components Analysis) and classification (Unweighted Pair Group with Arithmetic Mean Agglomerative Classification) techniques to floral-biometric, modern pollen trap and lake sediment pollen data situated within different rainforest communities in the tropical lowlands of Amazonian Bolivia. Modern pollen rain analyses from artificial pollen traps show that evergreen terra firme (well-drained), evergreen terra firme liana, evergreen seasonally inundated, and evergreen riparian rainforests may be readily differentiated, floristically and palynologically. Analogue matching techniques, based on Euclidean distance measures, are employed to compare these pollen signatures with surface sediment pollen assemblages from five lakes: Laguna Bella Vista, Laguna Chaplin, and Laguna Huachi situated within the Madeira-Tapajós moist forest ecoregion, and Laguna Isirere and Laguna Loma Suarez, which are situated within forest patches in the Beni savanna ecoregion. The same numerical techniques are used to compare rainforest pollen trap signatures with the fossil pollen record of Laguna Chaplin.

Differentiation between Neotropical rainforest, dry forest and savannah ecosystems by their modern pollen spectra and implications for the fossil pollen record

Accurate differentiation between tropical forest and savannah ecosystems in the fossil pollen record is hampered by the combination of: i) poor taxonomic resolution in pollen identification, and ii) the high species diversity of many lowland tropical families, i.e. with many different growth forms living in numerous environmental settings. These barriers to interpreting the fossil record hinder our understanding of the past distributions of different Neotropical ecosystems and consequently cloud our knowledge of past climatic, biodiversity and carbon storage patterns. Modern pollen studies facilitate an improved understanding of how ecosystems are represented by the pollen their plants produce and therefore aid interpretation of fossil pollen records. To understand how to differentiate ecosystems palynologically, it is essential that a consistent sampling method is used across ecosystems. However, to date, modern pollen studies from tropical South America have employed a variety of methodologies (e.g. pollen traps, moss polsters, soil samples). In this paper, we present the first modern pollen study from the Neotropics to examine the modern pollen rain from moist evergreen tropical forest (METF), semi-deciduous dry tropical forest (SDTF) and wooded savannah (cerradão) using a consistent sampling methodology (pollen traps). Pollen rain was sampled annually in September for the years 1999–2001 from within permanent vegetation study plots in, or near, the Noel Kempff Mercado National Park (NKMNP), Bolivia. Comparison of the modern pollen rain within these plots with detailed floristic inventories allowed estimates of the relative pollen productivity and dispersal for individual taxa to be made (% pollen/% vegetation or ‘p/v’). The applicability of these data to interpreting fossil records from lake sediments was then explored by comparison with pollen assemblages obtained from five lake surface samples.

Pollen-based biome reconstructions for Latin America at 0, 6000 and 18000 radiocarbon years

The biomisation method is used to reconstruct Latin American vegetation at 6000±500 and 18 000±1000 radiocarbon years before present (14C yr BP) from pollen data. Tests using modern pollen data from 381 samples derived from 287 locations broadly reproduce potential natural vegetation. The strong temperature gradient associated with the Andes is recorded by a transition from high altitude cool grass/shrubland and cool mixed forest to mid-altitude cool temperate rain forest, to tropical dry, seasonal and rain forest at low altitudes. Reconstructed biomes from a number of sites do not match the potential vegetation due to local factors such as human impact, methodological artefacts and mechanisms of pollen representivity of the parent vegetation.

Suppression of gliadins results in altered protein body morphology in wheat

Wheat gluten proteins, gliadins and glutenins, are of great importance in determining the unique biomechanical properties of wheat. Studies have therefore been carried out to determine their pathways and mechanisms of synthesis, folding, and deposition in protein bodies. In the present work, a set of transgenic wheat lines has been studied with strongly suppressed levels of γ-gliadins and/or all groups of gliadins, using light and fluorescence microscopy combined with immunodetection using specific antibodies for γ-gliadins and HMW glutenin subunits. These lines represent a unique material to study the formation and fusion of protein bodies in developing seeds of wheat. Higher amounts of HMW subunits were present in most of the transgenic lines but only the lines with suppression of all gliadins showed differences in the formation and fusion of the protein bodies. Large rounded protein bodies were found in the wild-type lines and the transgenic lines with reduced levels of γ-gliadins, while the lines with all gliadins down-regulated had protein bodies of irregular shape and irregular formation. The size and number of inclusions, which have been reported to contain triticins, were also higher in the protein bodies in the lines with all the gliadins down-regulated. Changes in the protein composition and PB morphology reported in the transgenic lines with all gliadins down-regulated did not result in marked changes in the total protein content or instability of the different fractions.

Nature of vegetation and building morphology characteristics across a city: influence on shadow patterns and mean radiant temperatures in London

Vegetation and building morphology characteristics are investigated at 19 sites on a north-south LiDAR transect across the megacity of London. Local maxima of mean building height and building plan area density at the city centre are evident. Surprisingly, the mean vegetation height (zv3) is also found to be highest in the city centre. From the LiDAR data various morphological parameters are derived as well as shadow patterns. Continuous images of the effects of buildings and of buildings plus vegetationon sky view factor (Ψ) are derived. A general reduction of Ψ is found, indicating the importance of including vegetation when deriving Ψ in urban areas. The contribution of vegetation to the shadowing at ground level is higher during summer than in autumn. Using these 3D data the influence on urban climate and mean radiant temperature (T mrt ) is calculated with SOLWEIG. The results from these simulations highlight that vegetation can be most effective at reducing heat stress within dense urban environments in summer. The daytime average T mrt is found to be lowest in the densest urban environments due to shadowing; foremost from buildings but also from trees. It is clearly shown that this method could be used to quantify the influence of vegetation on T mrt within the urban environment. The results presented in this paper highlight a number of possible climate sensitive planning practices for urban areas at the local scale (i.e. 102- 5 × 103 m).

The influence of vegetation and building morphology on shadow patterns and mean radiant temperatures in urban areas: model development and evaluation

The solar and longwave environmental irradiance geometry (SOLWEIG) model simulates spatial variations of 3-D radiation fluxes and mean radiant temperature (T mrt) as well as shadow patterns in complex urban settings. In this paper, a new vegetation scheme is included in SOLWEIG and evaluated. The new shadow casting algorithm for complex vegetation structures makes it possible to obtain continuous images of shadow patterns and sky view factors taking both buildings and vegetation into account. For the calculation of 3-D radiation fluxes and T mrt, SOLWEIG only requires a limited number of inputs, such as global shortwave radiation, air temperature, relative humidity, geographical information (latitude, longitude and elevation) and urban geometry represented by high-resolution ground and building digital elevation models (DEM). Trees and bushes are represented by separate DEMs. The model is evaluated using 5 days of integral radiation measurements at two sites within a square surrounded by low-rise buildings and vegetation in Göteborg, Sweden (57°N). There is good agreement between modelled and observed values of T mrt, with an overall correspondence of R 2 = 0.91 (p < 0.01, RMSE = 3.1 K). A small overestimation of T mrt is found at locations shadowed by vegetation. Given this good performance a number of suggestions for future development are identified for applications which include for human comfort, building design, planning and evaluation of instrument exposure.

Morphology induced spinodal decomposition at the surface of symmetric diblock copolymer films

Atomic force microscopy is used to study the ordering dynamics of symmetric diblock copolymer films. The films order to form a lamellar structure which results in a frustration when the film thickness is incommensurate with the lamellae. By probing the morphology of incommensurate films in the early ordering stages, we discover an intermediate phase of lamellae arranged perpendicular to the film surface. This morphology is accompanied by a continuous growth in amplitude of the film surface topography with a characteristic wavelength, indicative of a spinodal process. Using selfconsistent field theory, we show that the observation of perpendicular lamellae suggests an intermediate state with parallel lamellae at the substrate and perpendicular lamellae at the free surface. The calculations confirm that the intermediate state is unstable to thickness fluctuations, thereby driving the spinodal growth of surface structures.